/*
 * Copyright (c) 2009 Peter Troshin JAva Bioinformatics Analysis Web Services
 * (JABAWS) @version: 1.0 This library is free software; you can redistribute it
 * and/or modify it under the terms of the Apache License version 2 as published
 * by the Apache Software Foundation This library is distributed in the hope
 * that it will be useful, but WITHOUT ANY WARRANTY; without even the implied
 * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * Apache License for more details. A copy of the license is in
 * apache_license.txt. It is also available here:
 * @see: http://www.apache.org/licenses/LICENSE-2.0.txt Any republication or
 * derived work distributed in source code form must include this copyright and
 * license notice.
 */
package compbio.data.sequence;

import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
import static org.testng.AssertJUnit.fail;

import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.List;

import org.testng.annotations.Test;

import compbio.metadata.AllTestSuit;

public class SequenceUtilTester {

	@Test()
	public void testisNonAmbNucleotideSequence() {
		String dnaseq = "atgatTGACGCTGCTGatgtcgtgagtgga";
		assertTrue(SequenceUtil.isNonAmbNucleotideSequence(dnaseq));
		String dirtyDnaseq = "atgAGTggt\taGGTgc\ncgcACTgc gACtcgcGAt cgA ";
		assertTrue(SequenceUtil.isNonAmbNucleotideSequence(dirtyDnaseq));
		String nonDna = "atgfctgatgcatgcatgatgctga";
		assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));

		nonDna = "atgc1tgatgcatgcatgatgctga";
		assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));

		nonDna = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";
		assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));
		// String ambDna = "AGTCRYMKSWHBVDN"; // see IUPAC Nucleotide Code
		assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));

	}

	@Test()
	public void testCleanSequence() {
		String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";
		assertEquals("atgAGTggtaGGTgccgcACTgcgACtcgcGAtcgA".toUpperCase(),
				SequenceUtil.cleanSequence(dirtySeq));
	}

	@Test()
	public void testDeepCleanSequence() {
		String dirtySeq = "a!t?g.A;GTggt\ta12GGTgc\ncgc23AC\rTgc gAC<>.,?!|\\|/t@cg-c¬GA=_+(0){]}[:£$&^*\"t cgA ";
		assertEquals("atgAGTggtaGGTgccgcACTgcgACtcgcGAtcgA".toUpperCase(),
				SequenceUtil.deepCleanSequence(dirtySeq));
	}

	@Test()
	public void testisProteinSequence() {
		String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";
		assertFalse(SequenceUtil.isProteinSequence(dirtySeq));
		String notaSeq = "atgc1tgatgcatgcatgatgctga";
		assertFalse(SequenceUtil.isProteinSequence(notaSeq));
		String AAseq = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";
		assertTrue(SequenceUtil.isProteinSequence(AAseq));
		AAseq += "XU";
		assertFalse(SequenceUtil.isProteinSequence(AAseq));

	}

	@Test()
	public void testReadWriteFasta() {

		try {
			FileInputStream fio = new FileInputStream(
					AllTestSuit.TEST_DATA_PATH + "TO1381.fasta");
			assertNotNull(fio);
			List<FastaSequence> fseqs = SequenceUtil.readFasta(fio);
			assertNotNull(fseqs);
			assertEquals(3, fseqs.size());
			assertEquals(3, fseqs.size());
			fio.close();
			FileOutputStream fou = new FileOutputStream(
					AllTestSuit.TEST_DATA_PATH + "TO1381.fasta.written");
			SequenceUtil.writeFasta(fou, fseqs);
			fou.close();
			FileOutputStream fou20 = new FileOutputStream(
					AllTestSuit.TEST_DATA_PATH + "TO1381.fasta20.written");
			SequenceUtil.writeFasta(fou20, fseqs, 21);
			fou20.close();

		} catch (FileNotFoundException e) {
			e.printStackTrace();
			fail(e.getLocalizedMessage());
		} catch (IOException e) {
			e.printStackTrace();
			fail(e.getLocalizedMessage());
		}
	}

	/**
	 * This test tests the loading of horizontally formatted Jronn output file
	 */
	@Test
	public void loadJronnFile() {

		FileInputStream fio;
		try {
			fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "jronn.out");
			List<AnnotatedSequence> aseqs = SequenceUtil.readJRonn(fio);
			assertNotNull(aseqs);
			assertEquals(aseqs.size(), 3);
			AnnotatedSequence aseq = aseqs.get(0);
			assertNotNull(aseq);
			assertNotNull(aseq.getAnnotation());
			// System.out.println(aseq);
			assertEquals(aseq.getAnnotation().length, aseq.getSequence()
					.length());
			fio.close();
		} catch (FileNotFoundException e) {
			e.printStackTrace();
			fail(e.getLocalizedMessage());
		} catch (IOException e) {
			e.printStackTrace();
			fail(e.getLocalizedMessage());
		} catch (UnknownFileFormatException e) {
			e.printStackTrace();
			fail(e.getLocalizedMessage());
		}

	}

	enum Trial {
		one, two, three
	};

	/**
	 * This test tests the loading of horizontally formatted Jronn output file
	 */
	@SuppressWarnings("unchecked")
	@Test
	public void testMultiAnnotatedSequence() {

		FileInputStream fio;
		try {
			fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH
					+ "disembl.out");
			List<MultiAnnotatedSequence<DisemblResultAnnot>> aseqs = SequenceUtil
					.readDisembl(fio);
			assertNotNull(aseqs);

			/*
			 * MultiAnnotatedSequence ma = new MultiAnnotatedSequence();
			 * Map<Trial, List<Number>> val = ma.getInstance(Trial.class);
			 * List<Number> list = new ArrayList<Number>(); list.add(new
			 * Float(1.2)); list.add(new Double(5.662)); val.put(Trial.one,
			 * list); val.put(Trial.two, Arrays.asList(6.22f, 1, 37.6f));
			 * System.out.println(val); AnnotatedSequence aseq = aseqs.get(0);
			 */
			fio.close();
		} catch (FileNotFoundException e) {
			e.printStackTrace();
			fail(e.getLocalizedMessage());
		} catch (IOException e) {
			e.printStackTrace();
			fail(e.getLocalizedMessage());
		} catch (UnknownFileFormatException e) {
			e.printStackTrace();
			fail(e.getLocalizedMessage());
		}

	}
}